


of all the souls I have known

by la_muerta



Series: inevitable orbits [1]
Category: Shadowhunters (TV)
Genre: Alternate Universe - Space, Alternate Universe - Star Trek Fusion, Angst, BAMF Magnus Bane, Background Isabelle Lightwood/Maia Roberts, Canon-Typical Violence, F/F, Lightwood Siblings Feels, M/M, Mild Smut, Minor Character Death, Star Trek References, Starfleet Captain Alec Lightwood, Temporary Character Death
Language: English
Status: Completed
Published: 2018-08-07
Updated: 2018-08-07
Packaged: 2019-06-23 07:41:44
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 6
Words: 19,449
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/15601560
Author URL: https://archiveofourown.org/users/la_muerta/pseuds/la_muerta
Summary: Fighting for his life on an alien planet, Starfleet Captain Alec Lightwood can pinpoint the exact moment that his neatly-ordered life went to hell.It starts with a bar, and a beautiful stranger named Magnus.





	1. Chapter 1

**Author's Note:**

  * Inspired by [Highly Illogical](https://archiveofourown.org/works/14408865) by [la_muerta](https://archiveofourown.org/users/la_muerta/pseuds/la_muerta). 



> This was originally written as a one-shot for my [Fic Bingo team](https://archiveofourown.org/series/1000629), but it's changed somewhat during it's expansion.
> 
> Much love to my fabulous beta [Fatale](https://archiveofourown.org/users/femme/pseuds/Fatale) for fic massaging and Trek support! ♥
> 
> Beautiful cover art done by the wonderful [CryptidBane](https://archiveofourown.org/users/Impetus), and [trailer](https://www.youtube.com/watch?v=IrMLwa5Ggyg) made by the lovely [Catastrokey](https://archiveofourown.org/users/Catastrokey/pseuds/Catastrokey).
> 
> Written as part of the [Shadowhunters Hiatus Big Bang](https://shhiatusbang.tumblr.com).

 

 

 

 

 

 

_Stardate 2259.55_

_Earth, Sol System, Sector 001, Alpha Quadrant_

  

The bar was dark, noisy. There were too many rowdy academy cadets in their red uniforms jostling and shouting their orders at the bartender, too many visitors from other planets, too many Earth natives, just _too many_. Alec Lightwood was regretting every path and every decision that had led to him sitting at this tiny sticky table, his knees knocking the bottom of the table every five seconds because the people who furnished this bar had something against tall people, nursing a warm beer that had ceased to be drinkable half an hour ago. To be fair, most of his problems had stemmed from one very important and unfortunate decision that had been taken completely out of his hands: his parents' decision to adopt one Jace Herondale, now Jace Lightwood. Speaking of the devil...

"Don't you at least want to know my name before you reject me completely?" Alec heard Jace say a few feet behind him.

"I'm fine without it."

"You _are_ damn fine without it," Jace said with a leer and a wink at someone as he staggered towards Alec's table and slopped a third of his drink on it.

"Classy," Alec muttered, grabbing a couple of napkins from the holder to mop up the mess.

"You just wait, I'll snag one by the end of the night," Jace said, sweeping a lock of blond hair out of his eyes.

Alec sighed and didn't reply, because against all reason Jace _did_ always end up with at least one bedmate of somewhat female persuasion on his arm every night.

"What about you? Need some help?" Jace asked.

"With what?"

"Alec, seriously? We only get three months of shore leave, and you're just going to spend it sitting here, drinking alone?"

"No, you're right," Alec said, straightening up. "I should go home."

Jace snorted and pushed Alec back down onto his seat. "Fucking hell, man. I asked you out to have some fun so you wouldn't turn into stone inside your apartment, and you're going back to stick your nose in a history book."

"Your idea of fun is not my idea of fun."

"Nonsense. You just need to find the right guy. Here, let me help," Jace said, settling himself on the stool next to Alec, and Alec tried not to grind his teeth when Jace kicked his shin in his drunken clumsiness. "How about that one?"

Alec rolled his eyes. Jace grabbed Alec's head with both hands and forced him to turn his head in the correct direction.

"Pass," Alec muttered, glancing at the guy Jace pointed out.

"That one?"

" _Hard_ pass."

"Not into Tellarites and their sexy tusks? Ok, how about that one?"

Alec glanced in the direction Jace was indicating, then glared at Jace. "Now you're just being an ass."

Jace grinned and waggled his eyebrows suggestively. "Hey, tails are a lot of fun, believe me."

"I'll take your word for it, but that’s a woman."

"Really?" Jace said in surprise, squinting over his shoulder. "Well, in my defence, the lighting in here sucks. More for me, then."

"Have you satisfied your sudden urge to play matchmaker? Can I go now?"  

"No, Izzy said I wasn't allowed to let you off until you'd gotten the number of at least one guy."

_Izzy_. He should have known she'd be in on this. "She's one to talk, after years of insisting that she's perfectly happy being single," Alec grumbled.

"Yeah, but she's with Maia now."

Alec wasn’t sure what that had to do with anything, unless being in a happy relationship was a lot like joining a cult, in that it made you feel like you had to convince everyone else to get into a relationship too.

"I think she's just worried," Jace said. "You know what they say about you behind your back."

How could he not? Illogical as it was, since both Maryse and Robert Lightwood had been human, and Izzy was outgoing and vivacious, the whispers and rumours continued to follow Alec. They called him "green-blood" and "hobgoblin" - all slurs generally used for Vulcans. Just because Alec believed that rules existed for good reason, and because he thought decisions should be made on the basis of logic, not feelings. Starfleet was open to all species and races by law, but some prejudices ran deep. Vulcans would let you die if they thought it would serve a greater purpose, Romulans would make sure that if anybody had to die to serve a greater purpose it would be you, Klingons were just barbaric even if the Federation wasn't constantly at the brink of war with them, and so on. Trying to eradicate bigotry completely was a lost cause; they might as well have tried to demand that people weren't allowed to breathe.

"I don't care," Alec pointed out.

"Yes, yes. It's just jealousy, because you made officer in three years and got command of your own ship in seven years," Jace said placatingly. "Izzy isn't saying that you need to get with someone to prove that you're not who they say you are - she's saying you’d be happier if you had someone to share your joys and sorrows with. Her words, not mine."

"I have you and Izzy. It's enough," Alec said.

"Aww. That's so sweet I might cry," Jace said and grinned, slinging an arm around Alec's shoulders and leaning heavily on him.

"Asshole," Alec muttered, shoving him away.

"I told Izzy she didn't need to worry. Once you decide you want to put yourself up on the market, there'll be tonnes of people lining up - after all, you're a Starfleet Captain."

"Is that what you've been using to impress the girls?" Alec asked shrewdly.

Jace shrugged. "Ok, so maybe I've been fudging the details a bit. But 'Captain' just sounds better than 'First Officer'."

Alec shook his head in exasperation. "Fine, whatever. The sooner you find someone to bring home, the sooner I can get out of here."

 

\--

 

Alec watched his brother disappear into the crowd again with half a mind to just stand up and leave, and text Jace his apologies.

"May I take this seat?"

Alec turned around in surprise. The first thing he noticed about the man who had spoken to him was his eyes: gold-green and reflective like a cat's, with slit pupils that had dilated in the low light. Alec wondered if he was part-Caitian, which in turn reminded him about what Jace had said about tails, bringing a flush of colour to his cheeks. It didn't help that the stranger was very attractive, or that his shirt was so tight over sculpted arms and a broad chest that the buttons were threatening to fly off. The beautiful stranger was still looking expectantly at Alec, and Alec realised that he hadn't answered his question.

"Um, sure."

The stranger's smile widened. "Can I get you another drink?" Alec didn't want another drink, but he found himself nodding anyway.

The other man soon returned with a beer and a fancy cocktail in hand. "I'm Magnus."

"I'm Alec. Where are you from?"

"Oh, somewhere closer than you'd expect," Magnus said coyly. "But I wouldn't be opposed to having someone show me around. Things have changed so much since I've last been here."

They circled some frivolous topics of conversation, and Alec was pleasantly surprised to discover that Magnus was well-versed in many subjects, particularly history. They were soon deep into a discussion about the Eugenic Wars fought on Earth hundreds of years ago.  

"...my point is, that the Wars could have been avoided completely if the human race hadn't tried to play God," Alec said.

"So, in your opinion, the existence of the Augments was a mistake? They should never have been made?" Magnus asked, idly running a finger around the rim of his glass.

Alec shrugged. "What's done is done. But I think the greater mistake was assuming that they had any reason to see _us_ as the superior beings and fall in line."

Magnus opened his mouth to respond, only to be interrupted by the bartender, who had come up to tell them the bar was closing. Alec looked around in surprise at the almost-empty bar; Jace, of course, was long gone.

Magnus seemed equally surprised that they had lost track of time, but quickly recovered. "Time flies when you're having fun," Magnus murmured. "But the night is still young, don't you agree?"

Alec felt Magnus place a hand on his thigh under the table and swallowed hard. Their conversation had been easy and enjoyable, but with one move Magnus had changed the mood between them into pure electricity. It would be stupid to bring a stranger home, even one as alluring as Magnus - or perhaps it was a bad idea precisely because Magnus was just too good to be true.

Instead, Alec said: "My place is just a couple of blocks away."

"Perfect," Magnus said with a smile.

  

\--

  

Magnus had Alec up against the door before he could turn the alarms on properly, holding him in place with a hand tangled in his hair and a thigh slotted between Alec's legs before pulling him down for a hungry kiss. It was only a kiss, but Alec was already drowning in the sensations - the faint taste of whatever fruity alcoholic drink Magnus had been drinking, the press of Magnus' body against his, radiating heat. Alec moaned when Magnus sucked gently on his tongue, grinding down Magnus’ leg as he tried his best to tug Magnus' shirt out from where it was tucked into his too-tight pants so he could run his hands over the warm, smooth skin. Magnus scraped his teeth along the underside of Alec's jaw and down his neck, tasting him, learning him. Alec grabbed a handful of Magnus' ass to pull him closer (no tail, his brain helpfully supplied), rocking their hips together so their hardening cocks were rubbing against each other.

"I... I don't normally do this," Alec gasped when Magnus pressed his leg up a little more firmly on the sensitive spot behind his balls.

"Then aren't I special?" Magnus murmured before capturing Alec's lips again. 

Magnus stopped kissing Alec just long enough to get him out of his jacket and shirt, while Alec went straight for Magnus' belt buckle. Magnus allowed Alec to switch their positions around, watching with heavily-lidded eyes as Alec got to his knees. He tugged at Alec's hair, tilting his head back and urging him to look up him, then nudged Alec's lips with the tip of his cock. Alec opened his mouth and wrapped his lips around the sensitive head, kissing and licking it gently at first and moaning at the taste of precome blooming on his tongue. Then he relaxed his jaw as much as he could and started sliding down, taking more of Magnus slowly, never breaking eye contact with Magnus.

His hands went to Magnus' thighs, encouraging Magnus to fuck his mouth, fingers digging into hard muscle as he fought to breathe around the weight of Magnus' cock on his tongue. He moved his tongue from side to side as much as could, sliding it along the ridge of the sensitive head until he had Magnus bucking and gasping. Magnus kept his eyes on him, lips parted in pleasure and breathing increasingly laboured as Alec increased his efforts, sucking harder and struggling to take even more of Magnus until the tip of his cock was almost brushing the back of Alec's throat. Magnus tried to gasp out a warning, but Alec refused to pull off, and in a moment Magnus was coming inside Alec's mouth with a bitten-off shout of pleasure. 

Alec kept his mouth on Magnus, working him through his climax with gentle licks and sucks until Magnus began to tug at his hair again, urging him off. Alec sat back on his haunches and wiped his mouth with the back of his hand, feeling oddly accomplished. It had been far too long since he'd been with someone - he'd forgotten how good it felt to share pleasure with another person.

"I must say, it's not everyday that you get one of Starfleet's best and brightest kneeling before you," Magnus panted.

Alec froze. How had he known? Alec's occupation had never come up during their conversation. The realisation was like a bucket of cold water - of course the beautiful stranger hadn't really been attracted to _him_. Being a Starfleet Captain usually drew two kinds of reactions: admiration or resentment. He looked up uncertainly at Magnus, wondering if he'd just been played for a fool, wondering if Magnus - if that was even really his name - had just wanted the satisfaction of humiliating him.

Sensing his unease, Magnus immediately pulled him up and cupped his aching jaw gently. "I overheard your conversation with your First Officer," he admitted. "But you're not like the rest of them, are you?"

"What do you mean?" Alec asked, frowning.

"For one, you're the one who got on your knees first," Magnus said, slightly teasing. "Doesn't it bother you, that I am not fully human?"

"No, it doesn't. Why would it?"

Magnus seemed surprised by the strength of his conviction. "Then things have truly changed a lot on Earth."

"Well, there are still some people with outdated ideas about the superiority of the human race, of course," Alec said frankly. "But I don’t think there’re many of them, and the Federation is here to stay whether they like it or not. They’re just a powerless minority."

"Maybe they are. And it would be best if they remained that way," Magnus murmured, and when he smiled at Alec again, it didn't quite reach his eyes. "But enough of that. I believe I owe you one," he said, reaching for Alec's belt loops.

"No. No, I can't," Alec said, overcome by the persistent feeling of wrongness. "Magnus, if this isn't something you want..."

"Oh, I assure you that there's no way you can make me do something that I don't want to," Magnus replied, and Alec was sure he wasn't imagining the edge to Magnus' tone.

"I don't want to take advantage of you," Alec insisted. 

"You think that you are taking advantage of me?" Magnus repeated with a sharp bark of laughter, then grew serious. "That couldn't be further from the truth. Believe me when I say that I don't normally do this either."

To say Alec was confused would have been putting it mildly, but he let Magnus pull him closer again.

"Take me to bed, Alexander," Magnus whispered against his lips, then kissed him fiercely. 

Alec couldn't quite remember how they got to his bedroom, or how he'd managed to get Magnus out of those damned pants. All he remembered after that was skin on skin, their hands, lips and tongues exploring every inch of each other's bodies. Magnus laid Alec on the bed like he was afraid he might break him, and settled himself over Alec, pressing him into the mattress. Magnus let Alec kiss all the strange scars on his arms and torso, as if he could erase all the old hurts now; then he claimed Alec's lips and kissed him until he couldn't think, couldn't breathe, feeling like he'd been turned inside out and upside down. And when Magnus finally sank down onto his cock, it was all Alec could do to not come on the spot.

"Magnus, _Magnus_... I can't-" Alec gasped as Magnus began to ride him in swift, easy strokes.

"Then don't. Just let go, Alexander," Magnus panted.

Alec could only surrender to the inexorable tidal wave of pleasure pulling him under, and came with Magnus' name tumbling from his lips.

 

\--

 

Alec woke up to bright morning sun and cold sheets on the other side of the bed.

When had Magnus left? They'd arrived at Alec's apartment shortly after two in the morning, and it had been almost daybreak when Alec had not so much fallen asleep as dropped into the oblivion of exhaustion, completely spent and boneless from the number of orgasms Magnus had wrung out from him. He must have been so out of it that he hadn't even noticed Magnus leaving, sleeping through the safety alarms that Magnus shouldn't have known how to disarm - except that he suddenly recalled that he'd been too distracted by Magnus to even turn them on when they'd come in last night.

He sat up, wincing from how battered his body felt, even though he could tell that Magnus had tried to be gentle - alien strength was always a wildcard. He strained his ears for any sign that he wasn't alone in his spartan apartment, half hoping that Magnus was just in the washroom. His clothes were still littered all over the floor, but there was no sign of Magnus' more flamboyant clothes, or the various rings that Magnus had pulled off his fingers in a hurry last night and scattered carelessly all over Alec's nightstand. Then Alec spotted writing on the electronic notepad on his nightstand. The note had been written with a looping flourish: _I'm sorry I had to leave without saying goodbye. -M_

Nothing else.

Alec bit his lip, worrying the stylus of the notepad absently. It was his own fault, of course, for hoping that this could be more than just a one-night stand, and it hurt that Magnus hadn't even left any means of contacting him again. How had he read Magnus' intentions so wrong? Had he imagined the connection he'd felt between them? Typical. The one time he'd let his heart override his head, he'd been reminded of why that was always a bad idea.

His communicator went off, interrupting his downward spiral into self-pity. He checked the caller ID and frowned when he saw that it was his superior, Rear Admiral Hodge Starkweather.

"Sir?"

"Emergency meeting in Starfleet Command at oh-nine-forty-five hours, Lightwood. Starfleet is under attack."

 

 

 

 


	2. Chapter 2

 

 

"How was last night?" Jace whispered.

" _Seriously_ not the time for this," Alec muttered back, thankful for the high collar of his dress uniform hiding all the bruises Magnus had sucked into his skin.

"Is everything alright, gentlemen?" Admiral Morgenstern asked from the head of the table.

"Yes, sir," Alec replied quickly.

Admiral Valentine Morgenstern was the head of Starfleet, a cold, calculating man who had been friends with Alec and Jace's parents when they were alive. Alec didn't like him much, and he was certain the feeling was mutual, especially after Alec had spoken up against the Admiral's proposal to divert more of Starfleet's research and development spending towards aggressive weaponry instead of defence and warp technology. So far they'd mostly stayed out of each other's way, and Alec was fine with that. But Alec was only far too aware that as the youngest captain on Starfleet, too many people were expecting him to screw up.

Across from them, Hodge Starkweather was shooting them a chastising look, which Jace responded to with a cheeky grin. Hodge was also an old family friend, but he'd remained involved in their lives even after the deaths of Stephen and Céline Herondale, and later Robert and Maryse Lightwood, taking over the guardianship of Alec, Izzy, and Jace until they'd come of age. They had all been in their late teens by then, and Hodge was only older by a decade or so, so he hadn't been a father figure as much as an older brother of sorts. It was Hodge who had encouraged all of them to join Starfleet in the footsteps of their parents, and Hodge who had recommended Alec for the position of Captain of the USS Archer, with Jace as his First Officer.

"As I was saying," Admiral Morgenstern continued with a pointed look at Alec and Jace, "by now, most of you should have heard about what happened in downtown New York. At around oh-seven-thirty hours today, a Starfleet data archive was bombed and razed to the ground. Forty-two good men and women are dead."

The Admiral tapped on a screen in front of him, and the screens in front of everyone else came to life, playing the security footage from a street camera. Alec recognised the place - it had been a church once, now repurposed as a library focussing on Earth's pre-warp history. There was nothing left of the building, the streets filled with screaming and crying people as ash rained from the sky, and Admiral Morgenstern tapped on his screen again to zoom in on a particular point in the video - a figure in a red trench coat studded with rhinestones in the back that Alec immediately found achingly familiar, getting into a police-issue emergency evacuation jumpship he had presumably stolen. The camera zoomed in closer, and Alec's suspicions were confirmed when Magnus' face filled his screen.

"We suspect that this is the man responsible for this act of terrorism. For unknown reasons, he has just declared a one-man war against Starfleet," the Admiral said, but Alec was finding it impossible to pay attention.

He glanced out of the floor-to-ceiling windows that took up more than half of the room's wall space, at the unobstructed view of New York and all its skyscrapers of glass and steel reflecting the late morning sun. They were high above the hustle and bustle of the city, since the Starfleet Command conference room was at the 180th floor of the Starfleet HQ - the topmost floor - and Starfleet HQ was easily the tallest building around. He'd had Magnus in his bed, in his arms, not more than a few hours ago. It seemed ridiculous to think that Magnus had slipped out of his bed in the wee hours of the morning, then gone straight on to murder a few dozen innocent men and women in cold blood. Unless, of course, he'd wanted to be in Alec's bed for another reason...

"The perpetrator was dressed in the uniform of a Starfleet captain, so nobody thought to stop him," Admiral Morgenstern continued, and Alec had a sinking feeling that if he went back to his apartment to check his wardrobe, he would find that he was missing one set of his captain's uniforms.

"We also found the body of a Starfleet officer nearby - a member of my own crew, Lieutenant Emil Pangborn. His thumb had been cut off, and one of his eyes gouged out so the perpetrator could get past the biometric scanners."

Alec's eyes snapped forward at that. He'd been asleep when Magnus had left, completely at his mercy. Magnus could have taken _his_ eye and thumb, instead of going to the trouble of attacking another Starfleet officer - so why hadn't he?

"You need to get past biometric scanners to go into the library?" Jace asked Alec in a whisper, oblivious to his brother's mental turmoil.

"Shhh!"

"What? It's not like I've ever been in one, how the hell am I supposed to know?"

Admiral Morgenstern shot the two of them another dirty look before continuing. "All of you gathered here today represent the senior command of all the vessels in the region, and under no circumstances are we to allow this man to escape Federation space. Earth's perimeter sensors have not detected any warp signatures leaving the planet, so we know he can't be far. We don't know who he is or why he has done this, but he has shown willingness to kill innocent people, so the rules of engagement are simple: if you come across this man, you are authorised to use deadly force on sight."

Except that it didn't add up. Jace was right - you didn't need security clearance to go into the library, because everything in there was public record. Unless there was more to the data archive than met the eye, there was no reason for anybody to target it. Magnus had tried to get close to him for a specific purpose, and if he'd originally intended to sneak in pretending he was a member of Starfleet, why had he then destroyed the data archive in such a showy way?

Alec's eyes went back to the screen in front of him, trying to understand. Magnus was looking straight at the camera, so he'd known it was there, and Alec just couldn't reconcile that expression on Magnus' face with that of a cold-blooded murderer. Magnus looked furious, but also devastated, his eyes red-rimmed and full of sorrow. Bombing the data archive was a message, and Alec would bet that if Magnus had intended to make a quick getaway after sending that message, he'd have been long gone.

"Sir, was anything else housed in the same building as the data archive?" Alec asked.

The Admiral frowned, displeased that Alec had interrupted him in the middle of allocating positions in his strategy for the manhunt. "Excuse me?"

"It's just... why bomb the archive? And why did he need to sidestep biometric security?" Alec asked, plunging onward despite the disapproving looks he was getting from some of the other officers. "I’ve been to this particular archive many times before. You don't even need to scan your thumbprint to borrow material, just leave a name and contact number."

"Why does a mad man do anything?" Admiral Morgenstern countered.

"I agree with Alec," Jace chimed in. "If he'd really wanted to hurt Starfleet and kill lots of people, a data archive is the most boring place to target. I'm surprised there were even more than a handful of people in there so early in the morning."

"In the event of any sort of attack on Starfleet property, protocol mandates that senior command gather all captains and first officers at Starfleet HQ, in this room," Alec said slowly. Starfleet Command was on the top floor of Starfleet HQ, not easily accessible - unless, of course, one happened to have a jumpship at their disposal, specially made for the purpose of rescuing people trapped in inaccessible places...

Alec heard the whine of the jumpship's engine going over the roof seconds before it appeared outside the window and a beam of light shot through the glass, aimed right at where Admiral Morgenstern was seating. The Admiral threw himself into the floor just in time to avoid being blasted by the beam, and ducked under the table to avoid the next shot.

Screams of fear and pain began to fill the room as their assailant began to open fire on other people in the room. None of them were armed, since weapons were not allowed in the conference room, and the table and chairs were the only items they could take cover behind. The pilot of the jumpship had a clear view of the whole room - their best chance of survival was to get out of the room, where they wouldn't be sitting ducks.

"Get out! Everybody get out!" Alec shouted.

Jace was already heading for the only exit, a door that led to a private elevator only accessible to captains and first officers. As his brother fumbled with the security scanner, Alec dug out his communicator from his pocket and dialed emergency services.

"Starfleet Command conference room is under attack, we need back-up with air defence capability!" Alec shouted into the device, hoping that he could be heard above the chaos around him.

Alec pulled Jace down to the floor just before the next shot hit the security panel Jace had been fiddling with, showering them with sparks. Alec glanced up at the elevator's display and saw it fizzle out. They had to assume that they were all trapped in the room now, at the mercy of their attacker until reinforcements arrived.

"What do we do now?" Jace yelled.

Even if they had their hand phasers, they'd be useless against the jumpship, which had been built to protect the police from most common weapons. Alec's eyes lighted on the concealed fire safety panel in one of the walls.

"Get something stuck in the turbine of his engine. Wreck the craft and get it out of the air," Alec suggested. "I'll distract him."

" _You're_ going to be the distraction?" Jace replied incredulously, but got to his feet.

They made their way to the fire safety panel crouched low and stumbling over the prone forms of their fellow Starfleet officers. There was no time to check if they were dead or merely unconscious. Alec grabbed the fire extinguisher and left Jace to the rest of it, running to the centre of the room, right in front of the jumpship. The window glass here had been completely destroyed by the jumpship's inbuilt phasers, and Alec could see the face of the pilot clearly despite the tinted glass of the jumpship's plexiglass windshield. _Magnus_.

He didn't look surprised to see Alec, but he'd stopped firing on the room, and in those few seconds Alec wondered if Magnus might give up and leave if Alec continued to be a human shield for everyone in the room. But Magnus' face was set in grim determination, and Alec thought he saw in his eyes the exact moment that Magnus decided that Alec's life was too insignificant to spare a second time if it would jeopardise his greater purpose.

Alec emptied the contents of the fire extinguisher at the jumpship before Magnus could shoot him, his aim slightly off-centre, surrounding the jumpship in a haze of chemicals. It swerved away to the right just as Alec hoped it would, and he saw something fly right into the solo turbine underneath the jumpship, trailing a fire hose tail behind it. The whine of the engine intensified as Jace's missile tangled inside the engine, sparks flying as Magnus fought to keep his craft under control. The fire hose pulled taut, the spool of hose finally running out, and the jumpship teetered and screeched before pulling the entire fire safety cache out of the wall and straight into the turbine. The force of the impact sent the jumpship careening wildly, and Alec had a pang of regret when the engine exploded and the smoking craft began to fall - there was no way that Magnus would survive the crash. The smoke and the speed at which the jumpship was losing altitude meant Alec couldn't see into the cockpit properly to even catch one last glimpse of Magnus. He leaned out of the window to watch its fiery descent, and in the distance, he heard the wail of approaching sirens.

  

\--

 

There had been 26 men and women sitting at that conference table that morning, and almost half of them were now dead - including Hodge Starkweather.

Starfleet would be making the funeral arrangements, so at least that was out of his hands. Izzy had insisted on giving him and Jace a full medical checkup, but had ended up sobbing into his shirt about halfway through. He hadn't seen Izzy cry so hard since their parents and baby brother had died in a car accident, and Jace was trying to hide his sniffles by pretending he had a flu. Throughout it all, Alec had held on to one illogical thought: it was his fault.

He knew it didn't make sense. Magnus might have stolen his uniform as a disguise, but he could just as easily have stolen another officer's - after all, he'd also stolen someone else's eyeball and thumb. Alec hadn't leaked any classified information that had helped Magnus in his attack, and in fact he and Jace had been the ones to put a stop to Magnus in the end. There was no way he could have known that Magnus had been planning to bomb the data archive and open fire on a roomful of Starfleet officers when he'd invited him home to his bed. But knowing the facts and using them to rationalise his way through the survivor's guilt he felt were two different matters. It didn't change the feeling that he could have done _something_ , but he hadn't.

He supposed that maybe there wasn't really much point confessing to Admiral Morgenstern that the captain's uniform Magnus had stolen had been his. 'Magnus' probably wasn't even his real name, and nobody would know for sure now that he was dead. Still, Alec made his way to the Admiral's office after Izzy declared him as fit for duty, fully prepared to at least face demotion. Knowing Admiral Morgenstern's opinion of him, however, he thought it was more likely that he would be court-martialed.

"Who's that?" the Admiral called out irritably when Alec knocked on the door.

"It's Alec Lightwood, sir."

"Come in," Admiral Morgenstern replied, sounding a lot more pleasant, and when Alec opened the door he was surprised to see Jace already standing inside the office.

"Ah, Captain Lightwood. Just the man I was looking for," the Admiral said in a grave voice as Alec stepped into the office gingerly.

Alec had never had to call on the Admiral before this, and he couldn't help noticing that wasn't a single personal item in the enormous office - no photo frames, no decorations, not even a 'world's best dad' mug or something that would make the Admiral seem a bit more human. Even _Alec_  had something on his desk in his office on the Archer, a framed photo of his siblings that Izzy had gifted him - pretty unnecessary, seeing how they were both part of his crew and therefore constantly with him, even on the year-long exploration missions, but still he kept it there.

"I was just speaking to your brother about Hodge Starkweather. I'm sorry for your loss," the Admiral said. "Did you know that I was the one who talked him into joining Starfleet?"

Alec shook his head, glancing at Jace. He wanted to speak to the Admiral alone, but hoping that Jace would take a hint and make himself scarce was probably wishful thinking. "You wanted to see me, sir?"

"I wanted to commend the both of you for your quick thinking that day. You saved all of us," the Admiral said. "But I'm afraid the threat is not over."

"What do you mean?" Alec asked, frowning.

"This is classified information, I hope you understand," Admiral Morgenstern said, then waited for both of them to indicate that they understood the gravity of the matter before continuing. "We've kept this quiet from the rest of Starfleet so as not to cause panic and alarm, but the wreckage of the jumpship was empty. Our mysterious attacker is still out there, and I fear that this is just the beginning."

"What? We watched that jumpship go down, there was no way he could have gotten out of there," Jace protested.

"There was a strange device inside the ship, some sort of alien technology. We suspect it might be some sort of portable transwarp beaming device," the Admiral said.

"Sir, I have an engineer on my crew who is exceptionally talented. If Maia was given access, she might be able to give us some insight on the device," Alec suggested.

"Yes, I've heard of her. She's half-Klingon, is she not?" Admiral Morgenstern said. "In fact, you have one of the most diverse crews in Starfleet - you also have a Borg drone on your crew, don't you?"

"Former drone. Raphael was liberated from the Borg Collective. He's as human as you and I," Alec corrected him, frowning.

“Sure, if you ignore the cyborg parts and possible immortality,” Jace muttered, earning a glare from Alec.

"Of course," the Admiral said, flashing a smile that didn't quite reach his eyes. "Well, I'm sure your engineer is very capable, but I think my team has this covered. In the meantime, I want you to keep your crew on high alert. I think a single ship sneaking up on him will be more effective than a whole armada spooking our quarry. The moment we have any word on this bastard's location, I want you and your crew to go after him and bring him to justice. Are you willing to take on this assignment, gentlemen?"

"Yes, sir," Jace said immediately.

A chance to right his wrongs, handed to him on a silver platter?

"Yes, sir," Alec replied. "It would be an honour."


	3. Chapter 3

"Status report, Lieutenant Roberts," Alec spoke into his communicator as he got off the shuttle with Jace, both of them already dressed in their Starfleet uniforms.

"The USS Archer is ready whenever you are, Captain. But we have not been approved for launch," Maia said, sounding like she was about ten seconds away from ripping someone's face off.

Alec frowned. "I'll be right there." 

Most of the ships in the fleet were still in their places in the Starfleet spacedock, an immense orbiting facility that looked like an odd mechanical creature with six arms radiating outwards and was visible even from Earth. It was currently a few minutes to midnight - over 13 hours since the attack on Starfleet Command - and the spacedock was running on a skeleton crew at this time of the day. When Alec and Jace reached the loading bay of the USS Archer, Maia was facing off with a bunch of smug-faced officers and trying to stop them from loading what looked like more than seventy torpedoes onto Alec's ship.

"What's going on?" Alec demanded.

"Admiral Morgenstern has ordered that the USS Archer be equipped with these new long-range photon torpedoes for your mission," one of them said, holding out a tablet. "They are untraceable and would therefore be invisible to Klingon sensors-"

"Woah, hold up," Jace interrupted. "We're going into Klingon airspace? I thought you said we were going to Qo'noS."

"Look at a map some time, Lieutenant Commander Lightwood," Alec muttered. He turned back to the officer and tried to take the tablet, but the man seemed to think that Alec was just going to sign-off without question. Alec glared at him until he let go, and quickly scanned through the document. "Why do I need torpedoes on board my ship? My mission is to capture the fugitive and bring him back to Earth."

"Actually, your orders are to kill him, then return to Earth before the Klingons find your ship in their airspace," Admiral Morgenstern said from behind him.

"It's against Starfleet regulation to condemn a man to die without a trial," Alec bit out.

"Your orders have nothing to do with Starfleet regulation, Captain. This man is a terrorist, and he doesn't deserve to be a treated with honour - this is an assassination, pure and simple," the Admiral said coldly, his eyes scanning the crew milling around. "I had thought that you would be more eager to avenge the man who took your siblings in when you had nowhere else to go. Or was all that talk about honour just empty talk?"

Jace bristled beside him, but Alec gave the Admiral a thin smile as he signed off on the authorisation form. "My apologies, Admiral. I was just being cautious."

"No! Captain!" Maia protested.

"We have our orders, Lieutenant Roberts," Alec said calmly.

"Godspeed, Captain," Admiral Morgenstern said in approval, and Alec watched him go with a frown.

 

\-- 

 

Alec made his way onboard the USS Archer with both Jace and Maia hissing after him like angry geese.

"I don't care if he's our superior, I want to punch him," Jace fumed. "And what's up with that order to fire torpedoes at the Klingons?"

"Captain, this is a radioactive catastrophe waiting to happen. This ship is not built for military operation, and not equipped to fire such a large payload of torpedoes. Besides, these are photon torpedoes - they run on their own fuel systems, and for some strange reason the fuel compartments of these torpedoes are combination-locked, so I can't look inside to assess how they'll react to our own warp core. A subtle shift in magnetic output from firing these torpedoes could set off a chain reaction in the warp core which would kill every living thing on this ship," Maia said angrily.

"Calm down, Lieutenant. We're not firing anything," Alec said.

"What? Then why did you allow them onboard the ship?" Maia demanded.

The Archer's crew were darting around them, minding their own business and preparing the ship for departure, but Alec dropped his voice anyway, low enough that only Maia and Jace could hear him. "Something is wrong with this whole mission," Alec said. "Even if it weren't morally wrong to hunt him down like some sort of animal, we hardly need 72 torpedoes to kill one man. Qo'noS is uninhabited, but the Klingons are definitely going to notice us unloading a bunch of torpedoes onto one of their planets. Besides, since when does the Admiral make a personal trip down to the spacedock to see off a ship?"

"What do you plan to do, Captain?" Maia asked.

"You said the fuel compartments were locked, against normal protocol. But weren't there specifications in the system?"

"No. In fact, the entire research and development project does not even seem to exist."

Alec frowned at that. Undocumented weaponry development? "Is it safe to take one of them apart?"

Maia hesitated. "I will try my best, Captain."

"Thank you, Lieutenant," Alec said, nodding his acknowledgment as Maia saluted him before making her way down to engineering.

"What's going on?" Jace asked as they took the turbolift up to the ship's operation centre, shrugging out of their jackets as they went.

"The Admiral was looking for someone," Alec said quietly. "Keep an eye out for someone new amongst the crew, someone who shouldn't be here."

Jace nodded. "Got it," he said, then smirked. "Nice hickey, by the way."

"Oh for fuck's sake," Alec muttered, tugging futilely at the collar-less neckline of his uniform.

When Alec stepped into the operation centre, he found all his staff at their stations and getting ready for take-off.

"Captain on the Bridge!" their helmsman Simon announced cheerfully.

Alec's eyes were immediately drawn to the flash of bright red hair at the communication station. He frowned. "Who are you? Where's Lieutenant Brown?"

She stood up and held out a hand for a handshake. "I'm Lieutenant Clary Fray, sir. Lieutenant Maureen Brown was unwell, so I've been assigned to the USS Archer in her place as your temporary communications officer. These are my transfer orders."

While Alec was skimming through the document she had handed to him, Jace sauntered up to her to shake her hand.

"I'm First Officer of the USS Archer, Lieutenant Commander Jace Lightwood, but please call me Jace. Since you're our new communications officer, I guess that means you have a talented tongue, huh?"

Alec resisted the urge to roll his eyes.

"Has that line seriously ever worked for you? Even once?" their new communications officer scoffed, and turned her back on Jace.

Simon tried to hide his laugh with a cough and Jace thwacked him on the back of his head.

"Ow! Hey, it's not my fault that Fray has good taste in men," Simon said.

"Please conduct yourselves with more professionalism on my ship, gentlemen. Mr Lewis, do you know Lieutenant Fray?" Alec asked suspiciously.

"She's my best friend, sir," Simon said. "Uh, that's why I recommend her for duty when Lieutenant Brown got ill."

"Alright then. Welcome on board the Archer, Lieutenant Fray," Alec said.

"Flight check is completed and the warp core is primed, Captain," their navigator Raphael said.

Alec sat down on the captain's seat. This was his ship, his crew, the one place that always felt like home, but today everything felt wrong. The screen in front of him looked out into the vast darkness of space, and pinpricks of distant stars; but all he saw was a pair of cat eyes in his mind's eye. "Set course for Qo'noS, maximum warp, and let's go."

Simon, who had been having a whispered conversation with Clary, startled and quickly turned back to his station. "Yes, sir," Simon said, tapping on the controls.

"Some time this year, Lewis," Jace drawled, ignoring Alec's threatening growl.

"I'd like to see _you_ drive this," Simon muttered mutinously, and took them into warp.

 

\--

 

"So your plan is just to walk around until we find him? Seems like that might take a while, it's a big planet," Jace observed.

Alec shot him a withering look. "Qo'noS is a dead planet with no inhabitants. All we need to do is scan for signs of life, the way we do when we're on normal explorations, and narrow down the landing parameters."

"Ok, fair enough. And I know you're all about the rules, and the First Officer should stay on the ship if the Captain has to leave the ship, but I'm going with you," Jace said.

"Yes, of course. Besides, there's no way I'm leaving _you_ in charge of my ship," Alec said.

"Fuck you," Jace snorted, then at Alec's glare, amended, "Sorry - fuck you, _Captain_. Hey, we should bring the new communications officer with us."

Alec frowned. "This is a manhunt, not an opportunity for you to sexually harass the crew. The K'normian trade ship we confiscated on our last trip is pretty tiny, so I need every person we bring to count."

"We're going on a Klingon planet, and I know you said it's uninhabited, but wouldn't it be useful to have someone who speaks Klingon with us? You can't possibly bring Maia. If our people are horrible to her for being half-Klingon, it's nothing compared to what the Klingons will do to her."

"No, you're right," Alec agreed. "Lieutenant Fray, could I have a word with you, please?"

"Yes, Captain?" she asked as she approached him nervously.

"You're coming with us as part of the landing party, just in case. I need you to understand that this is a sensitive mission - one wrong move could lead to all out war with the Klingons, and I'm not having that on my watch."

"Really? That's great! I mean, yes, of course I understand, sir. But why would you need me?"

"I hope it won't come to that, but if we have any run-ins with the Klingons, we may need you to serve as a translator."

"Oh! I, uh..."

Alec took in her panicked expression and frowned. "You _do_ speak Klingon, right? I know that it's a mandatory qualification for passing the Xenolinguistics course, given our current tensions with Klingon."

"Yes, of course I speak Klingon," she replied quickly. "But I'm a bit rusty."

"I would have hoped that Lieutenant Lewis recommended you based on the merit of your abilities, not just because you are friends," Alec said coolly.

"No! It's not Simon's fault! I'm just a bit nervous because I haven't spoken it in a long time, that's all," she said.

"Don't be nervous, our esteemed Captain doesn't bite. I might, though," Jace interrupted, and flashed her what was probably meant to be a charming smile. She narrowed her eyes at him and straightened her shoulders.

"When do we leave, sir?" she asked Alec with determination.

Alec eyed her warily, but they didn't have much of a choice - Klingon wasn't exactly a language people learned for fun, and having someone who could speak even basic Klingon would be more useful than none at all. "Any time now, Lieutenant."

"But first you're going to have to take that red shirt off. We're going incognito," Jace said with a wink, and their new communications officer flounced off with a disgusted snort.

"One more inappropriate remark from you and I'm filing a complaint against you on behalf of Lieutenant Fray," Alec warned his brother exasperatedly, but Jace didn't get a chance to reply.  

"Captain, we are ten minutes away from our destination. The shuttle bay should have the trade ship fuelled and flight-ready by that time, so that we spend a minimum amount of time in enemy space," Raphael reported.

"Thank you, Mr Santiago. As of now, you are Acting Captain of the Archer. I leave her in your good hands," Alec told him, and stood up at the same time as Jace. "Come on, Lieutenant Fray. Lieutenant Fray?"

He looked over to find her whispering urgently with Simon again. She startled when she realised that Alec and Jace were both waiting for her.  

"Yes, Captain! Sorry, Captain!" she replied, and quickly got up from her seat.

If Alec had been the type to follow his gut feelings, he would have decided right then that Clary Fray was going to be more trouble than she was worth.

  

\--

 

As Alec had expected, their sensors detected only a single life sign, right in the heart of the ruins of a city that had once stood on the planet. From what Alec knew, the planet had once been the pride of the Klingon homeworld, a thriving, bustling hub of trade and the crown jewel of the Klingon empire, until the subterranean volcanoes that everyone had assumed were extinct had suddenly become active again. Now it was just a barren wasteland of ash and crumbling buildings, plagued by intermittent earthquakes and an atmosphere so laden with volcanic dust that Alec could hardly breathe.

Alec had landed the small trade craft in the lee of a rocky mountain on the outskirts of the sprawling city ruins, hoping that the dull colours of the craft would be enough to keep it hidden. He left one of his senior security officers, Lieutenant Keytower, to watch the craft, and the rest of the landing party - Alec, Jace, Lieutenant Fray, and another senior security officer, Lieutenant Langford - made the short trek through the ruins on foot. The Klingons had utilised the complex network of natural cave formations on Qo'noS to build the foundations for their city, and the sensors indicated that Magnus was hiding in there somewhere despite the clear risk of being trapped or killed by cave-ins. Unfortunately, this also meant that they now had an entire underground maze to search, with limited time on their hands.

"Don't you wish you'd just fired the damned torpedos in his general direction instead?" Jace said as they entered the dusty gloom of the caves. His voice echoed faintly along the dark tunnels - the entire party froze, but Jace went on ahead for a few feet before he realised the rest of them had stopped. "Why aren't you guys moving?"

"You're giving our position away," Alec hissed.

"Oh, come on. We can't hang out in here all day. If he hears us, all the better - either he makes a run for it, and hopefully he'll get lost in this godforsaken shithole, or he'll come at us and we can end him and all get out of Klingon before we have much bigger problems than some madman with anger management issues," Jace said, ignoring Alec's repeated attempts to get him to keep his voice down.

"You seem very certain that you'll win," Fray observed. "Didn't he take out an entire roomful of officers on his own?"

" _Unarmed_ officers. People like him are cowards," Jace replied, then shouted into the darkness at the top of his lungs, "Cowards, you hear me!"

Alec ground his teeth and wondered for the umpteenth time what he had ever done to get saddled with Jace. "We're not shooting to kill," Alec said firmly.

"What? Then what do you plan to do?" Jace asked in surprise.

"We're going to capture him alive and bring him back to Earth to stand trial for his crimes," Alec replied.

"What, you think he's going to just throw down his weapons and come quietly? His phasers aren't going to be set to stun, and neither should ours!"

Why _did_ he think that there was a chance that Magnus would listen to reason? Because of a conversation in a pub, a one-night stand and a little show of mercy? Maybe Alec just hadn't had the right access for Magnus to want his eyeballs. After all, he'd barely hesitated before deciding to shoot Alec at the attack on Starfleet Command.

"We are representatives of the Federation, and we will follow the law of the Federation," Alec said.

"And Admiral Morgenstern's orders?" Jace asked, raising an eyebrow at him.

"The Admiral will just have to deal with me as he sees fit after we get back to Earth," Alec said grimly.

Like everything else on the planet, the caves were as dead and dry as a desert, more like a series of claustrophobic interconnected tunnels with low ceilings that occasionally forced Alec to duck his head. Alec was thankful for small mercies - at least in here it was only dark, not dark and _damp_. They searched the winding network of caves for almost an hour, and even with the sensors pointing the way, they saw no sign of Magnus - he always seemed one step ahead of them, and a couple of times he led them into a dead end, only to inexplicably appear on the sensors in a totally different direction. Wary of being led into a trap deep in the caves, Alec was just about to pull them out of the search and regroup to come up with another strategy when his communicator flared to life.

"Keytower?"

"Captain, the Klingons are coming!"

Alec cursed under his breath. "How many, and how far away are they?"

"At least three ships, sir. They've just entered Qo'noS airspace."

"Thank you, Lieutenant. We'll be there shortly." Alec cut the call, then announced, "We have to leave, quickly."

"What about our target, sir?" Langford asked.

"Geez, just tell Maia to let us fire half a dozen of those fancy photon torpedoes at this damn mountain and we'll be done with it. It's not like we're unloading all the 72 torpedoes, Maia is overreacting," Jace said dismissively.

"Unless you've suddenly become my chief engineering officer, _shut up_ ," Alec snapped. "Let's go."

When they reached their ship, Alec saw that it was too late. Their little borrowed craft was surrounded by Klingon vessels, and the Klingon troops standing at attention all around - every soldier at least as tall as Alec, and heavily armoured - outnumbered them ten to one. There was no way they were getting out of this fix by brute force; they would have to rely on a bit of cunning and diplomacy.

"I thought you said this sector was uninhabited?" Jace whispered, and Alec could only shrug.

The Klingons had dragged Keytower out of the ship and were interrogating him, and as they watched, the Klingon officer sneered and gestured to his men, and one of the Klingons holding Keytower down broke his arm, making him yell out in pain. 

"Sir, we need to get back to the Archer," Langford muttered. 

Alec shook his head; if they led the Klingons back to the Archer, the Federation would be implicated. Besides, they couldn't leave Keytower behind. "Remember, we're just K'normian traders hunting down a fugitive to claim the bounty on his head," Alec told his crew. "Lieutenant Fray, we're counting on you."

He led the way, coming out from behind the crumbling wall they'd been using as a hiding spot, holding his arms up to show that he was unarmed and putting on an expression that hopefully passed for unthreatening. Fray began speaking, and while the Klingons had initially seemed surprised that a human could speak their language - surprised enough not to open fire immediately - the expressions on their faces grew increasingly hostile. Alec had tried to learn Klingon, and he knew that it wasn't the easiest language, but Fray was much worse than "rusty". He only recognised a handful of Klingon words, most of them picked up from Maia when she was in a mood and started swearing, and he was pretty sure the word Fray had just used, " _taHqeq_ ", didn't mean what she thought it meant. 

He grabbed her and pulled her out of the way before the Klingon officer fired a shot that scorched the ground she'd been standing on mere seconds ago. Alec's hand dropped to the hand phaser hidden in the bulky coats they'd been wearing as a disguise, but his fingers had barely brushed his weapon when a ball of pure energy came out of nowhere and blasted the Klingon officer before he could take another shot, followed by a series of blasts that took out all the other Klingon officers with deadly accuracy. Alec had never seen weaponry like that, couldn't even see where the shots were coming from. The Starfleet crew drew out their phasers, and joined in the fray.

The Klingons didn't know who to start dealing with first, their attention torn between Alec's crew and the mysterious interloper, and their hesitation cost them at least one platoon of troops. Even then, they were still grossly outnumbered, and Alec could see more patrol ships descending on them. He ran forward to get to Keytower, planning to at least get him inside the shelter of their borrowed ship. But he had barely managed to take a few steps with Keytower leaning heavily on him for support when they were blindsided by a large Klingon soldier. They were both knocked to the ground, and Keytower never stood a chance - the Klingon ran through him with his Gin'tak spear before Alec shot their attacker point blank in the head.

"Keytower?" Alec checked his pulse, but he was already dead. "Fuck!"

Alec looked around, scanning the chaos for a glimpse of the rest of his crew, but their scuffling had kicked up the volcanic ash all around, making everything hazy. A patrol ship swooped low, raining gunfire on him, and Alec ran as fast as he could to seek shelter behind the structural remains of a building. The ship sent blast after blast, obviously determined to get him even if it had to wear the building down to rubble, and Alec cast about frantically for another place to take cover behind as the stone walls crumbled around his ears and showered him with sharp rock fragments that cut into his face and hands. Then there was a sudden _whoosh_ , and to his amazement, a huge ball of energy hit the patrol ship on the underside - the ship lit up with sparks as the circuitry went out and spun wildly, slamming into the ground with a deafening explosion.

Alec stared in shock. What the hell was that? He had never heard of a weapon powerful enough to take out a Klingon patrol vessel like that. He had to find the source of the energy blasts, _right now_.

Carefully navigating the narrow gaps between the ruins to stay out of sight from Klingons, Alec soon spotted him - a lone figure in a long, dark coat, spinning around to throw blasts of energy at the Klingons. Whatever weapon he was wielding had to be very small, because Alec couldn't see anything in his hands. But Alec had forgotten about trying to figure out what kind of weapon it was, because their mysterious rescuer was none other than Magnus.

Alec watched, transfixed, as Magnus wreaked havoc on the Klingon forces, firing blast after blast from his hands with extraordinary precision. A second patrol ship swooping down to join the fight on the ground was taken out, then a third was sent crashing after Magnus' blast turned it into a fireball. Then he saw it - the tall shadow moving behind Magnus, a Klingon soldier attempting to sneak up on Magnus...

Alec was running towards Magnus with his phaser out, but before he could reach him, a shrill female voice shouted, "Magnus, behind you!" and Magnus turned just in time to take out his would-be assailant. 

That voice - Alec recognised that voice...

But Alec had blown his own cover rushing out to Magnus' aid, and was promptly tackled to the ground by a huge Klingon soldier - his phaser was jolted out of his hand and skidded a short distance away. His attacker pinned him to the ground and drove his serrated kut'luch blade down, but Alec managed to grab his attacker's wrist. The point of the blade was an inch from his face; Alec twisted the wrist of his attacker, forcing him to loosen his grip on the knife, and at the same time someone came up behind the Klingon soldier to deliver a swift kick to his temple, sending him sprawling. Jace shot Alec's attacker quickly, then held out a hand to help Alec up. Alec was relieved to see that his brother looked relatively unscathed.

"You owe me a beer when we get back to Earth," Jace said cheerfully.

The tide of the battle had turned. With Jace fighting by his side, they managed to finish off another dozen Klingons before Alec suddenly realised that everything had gone quiet.

"Is that it? Did we get all of them?" Jace asked.

Alec shrugged. "Where are Langford and Fray?" 

"I lost sight of Fray," Jace admitted worriedly. "But Langford is dead. I saw one of them take his head off."

They stepped out into the open cautiously. A movement to Alec's left had him turning sharply, but it was just their new communications officer coming out of her hiding place, looking shell-shocked but otherwise unharmed.

"Clary! Get behind me," Jace said, moving to shield her.

Magnus was still standing where Alec had last seen him, but he started striding towards them once he spotted them. Jace and Alec raised their phasers, but Magnus didn’t seem to care. 

"Stand down!" Jace shouted.

Magnus stopped. He was a few feet away from them, but made no move to attack them, his hands seemingly empty. "Are the torpedoes intact?" Magnus asked quickly.

"What?" Jace asked, puzzled.

"I overheard you talking in the caves. The 72 torpedoes, the weapons you were thinking of firing at me. Are they are all intact?” Magnus asked urgently. 

“None of them have been fired,” Alec replied.  

Magnus’s gaze flickered to Clary, then he relaxed imperceptibly. "I surrender," he said, and held up his hands. Alec couldn't help noticing that Magnus really was empty handed - so where the hell was his weapon? 

Jace stared at him, slacked jawed. Alec stepped forward. "On behalf of Starfleet, I accept your surrender."

Magnus flashed him a sardonic smile. "Cuff me, then, Captain Lightwood, and bring me onboard your ship. I promise I'll behave."


	4. Chapter 4

 

  
The trip back to the Archer on the borrowed K'normian ship was a tense one. Jace kept his phaser trained on Magnus, hardly blinking, but Magnus didn't seem bothered by his hostility. In fact, he had his eyes closed and seemed to be... meditating?

It didn't escape Alec's notice that Clary Fray seemed to be "meditating" as well.

Once they stepped off the ship, there was a troop of security officers waiting to escort Magnus to a cell in the brig.

"Wait," Alec said. "Please escort Lieutenant Fray to the brig as well." Clary stared at him in surprise, but Magnus looked thoughtful.

"What?" Jace exclaimed. "Alec, have you lost your mind?"

"Clary Fray, you are not who you say you are. A communications officer who can't speak Klingon? You exploited your friendship with Lieutenant Lewis to get on this ship - or Lewis is in on this as well," Alec said gravely. "Would you care to explain yourself?"

Clary's mouth opened and shut a few times as she tried to find the words to defend herself, before she evidently gave up and decided to go for the truth, or at least some version of the truth. "Fray is my mother's maiden name. My name is Clarissa Morgenstern."

"You're the Admiral's daughter?" Alec asked, and she nodded.

"But that's all Simon was hiding from you, I swear. I told him I needed to get away from my dad, and between him and Maureen they came up with the idea of having me take Maureen's place. I used my father's access to forge the transfer documents. I'm a cadet in the Xenolinguistics course so I thought I would be able to handle it… I didn't mean to mess the mission up for you today," she said earnestly.

“Your lies caused the deaths of two men today,” Alec said, trying to keep his anger in check.

She looked shocked, like it had just occurred to her that those deaths were on her. “I… I take full responsibility, sir,” she said in a small voice.

"And that's all that you're keeping from me, the fact that you were hiding on my ship to avoid your father?"

"Yes," she insisted.

"And yet you know our fugitive by name," Alec observed. Clary's mouth fell open in surprise. "Gentlemen, please escort Miss Morgenstern to the brig," Alec said, dismissing them and making his way to the bridge.

Jace, who had just recovered from his shock, was trailing after him in uncharacteristic silence until he stopped short. "Wait - that means _you_ know his name as well."

Alec sighed. He knew Jace wasn't as stupid as he pretended to be, but he really did have the most inconvenient timing for remembering how to use his brain. "Yeah, he's the guy I met at the pub that night," he admitted.

" _Fuck_."

"You can say that again."

"Of all the people in the goddamned universe. No wonder you don't date," Jace muttered.

"Captain!" Simon greeted them as they walked in, then frowned when he noticed that Clary wasn't with them. Alec watched the realisation slowly dawn on Simon, that they'd been busted. "Oh shit. Captain, it wasn't Clary's fault. I was the one who suggested that she could switch with Maureen to get away from her dad."

"And what about her connection to Magnus?"

"Mag-who?" Simon asked in confusion.

"The man we're hunting down."

"What?! No! Clary would never!" Simon protested. "She's the kindest, sweetest person I know!"

Alec seriously doubted that, but he'd had Simon as his helmsman on the USS Archer for close to two years now. Simon was overly talkative, overly cheerful, and always forgot to disengage the external inertial dampener before warp, but he'd grown on Alec. Two years was a long time to be in close quarters with someone without building some sort of trust, and in a way Alec's crew had become an extended family. He'd trust any of them with his life, even the surly and taciturn Raphael. If Simon said he didn't know, then he didn't - he was a terrible liar, anyway.

"Whatever it is, we lost two good men today. Your friend has been taken into custody in the brig until I've had a chance to question her, and I promise she'll be dealt with fairly. As for you, unfortunately we need to get out of here before more Klingon patrols find us and you're the best we've got right now. When we get back to Earth, we'll discuss your suspension," he said sternly.

"Yes, Captain," Simon said meekly.

"Take us to warp, Mr Lewis. Mr Santiago, could I trouble you to take over the communications post as well for now? Contact Starfleet and let them know we have our fugitive alive and in custody, and we'll be on our way back to Earth so he can stand trial."

"Aye, Captain," Raphael replied, then Simon cleared his throat.

"Um... Captain? I'm not sure what happened, but the warp core isn't responding," he said nervously.

"Did you remember to disengage the external inertial dampener?" Raphael asked.

"Yes! Oh my god, it was just that one time, will everyone stop harping on it?!" Simon griped.

Alec scowled and tapped on the console at the Captain's chair. "Lieutenant Roberts."

"If you're asking about the torpedoes, I haven't been able to crack the combination lock, but I suspect something has been hidden inside some of them. I'm planning to deactivate the warheads to take a closer look," Maia said.

"No, Mr Lewis says the warp core isn't responding. Could you please check what's going on down there?"

After several minutes, Maia responded. "We've been sabotaged, Captain," Maia said grimly. "I'll need to go into the reactor chamber to realign the warp core manually. It’s a delicate operation - it might take a while."

"Alright, and be careful, Lieutenant," Alec signed off, mental gears spinning.

The damage had been done subtly, so that the warp core would bring them into enemy space but malfunction when they were trying to make their escape and strand them here. He had no doubt that it had happened when the torpedoes were being loaded on the Archer - and all signs pointed to Valentine Morgenstern, especially now that his daughter had mysteriously turned up on Alec's ship.

"Mr Santiago, has there been any rise in communication between Qo'noS and the orbiting Klingon surveillance and defence stations?

"Nothing, sir. All communications appear to be normal."

"Any sign of patrol vessels?"

"It's all quiet to a safe distance and beyond, Captain."

Alec heaved a sigh of relief - for now. Hopefully engineering would be able to get them out of this fix before the Klingons noticed them. "Jace, come with me. We're going to find out what the hell is going on."

 

\--

 

"It doesn't make sense," Jace repeated for the umpteenth time. "Why would the Admiral sabotage our ship?"

"Too many things don't add up and I don't trust the Admiral one bit," Alec said, keeping his voice low. "Why did he approach you instead of me when he wanted us to go on this mission?

"Because I'm the stupid one, and you're the smart one?" Jace guessed.

"You're the one who said it, not me."

"And I repeat, fuck you," Jace retorted as they rounded the corner to the brig, where Magnus and Clary had been imprisoned in separate cells, both with a plexiglass wall in the front that allowed the guards to monitor their every movement.

Magnus and Clary were both "meditating" again, Alec observed sourly. Magnus opened his eyes when Alec approached, so calm and composed sitting on the cot in his cell - nothing at all like the image of a violent terrorist who had slaughtered the men and women in Starfleet Command like it was nothing. Clary got to her feet, wiping away tears and adjusting her uniform nervously when Alec came in, but Magnus just eyed them watchfully. Alec sent Jace to speak quietly to the guard to leave them alone with their prisoners before approaching the plexiglass wall warily.

"Captain, I think my father has damaged your warp core," Clary said urgently.

"I know," Alec said. "Perhaps you would like to give us some insight why?"

But it was Magnus who replied instead. "Because your Admiral wants to use you as an example - of how treacherous non-humans are, and why they must be exterminated from Earth. He wants the Klingons to find your ship and declare war on Starfleet and to make you out as a traitor."

"How would you know that?" Alec demanded.

"Valentine Morgenstern is the leader of a group that calls itself Terra Prime. Their goal is to remove all non-humans from Earth and break away from the United Federation of Planets. I have heard him speak of you, none of it complimentary, but I didn't realise who you were until Clary told me. He says you are part-Vulcan; but I cannot see how that might be," Magnus said, then flashed him a wicked smile. "Unless you were holding back your strength that night."

Alec flushed, but it was Jace who jumped to his defence. "Shut your mouth," Jace seethed. "You're a monster! We were given orders to execute you on sight! The only reason you are still alive is because Alec is allowing it."

"Jace," Alec chided him. His gaze flickered back to Magnus. "Why did you save us, back on Qo'noS? What's in the torpedoes that would make you give up your freedom and come quietly? My chief engineer tried to open one of them-"

"Oh no! You can't open them!" Clary said frantically.

"Why not?" Alec asked, frowning.

"Because one of the torpedoes contains a device I stole from my father - the Genesis Device," Clary said. "It's something Magnus invented, and it could destroy an entire planet."

"And _you_ made this thing?" Jace asked Magnus angrily. "How are you not a monster?"

"The Genesis device was meant to transform an uninhabitable planet at a subatomic level, to make it suitable for humanoid life - for my crew," Magnus replied coldly.

"Your crew?" Alec stared, then it clicked - how insistent Admiral Morgenstern had been about using the torpedoes, Maia's suspicions, and how agitated Magnus had been. "The rest of the torpedoes - are you saying that there’re _people_ inside the torpedoes?"

"What the hell are you?" Jace barked out.

"Jace, you're not helping," Alec said with forced patience. He turned to Magnus. "Where are you from? Where is your homeworld?"

Magnus considered him carefully, then replied, "Earth."

"Then why do you have to leave?"

"We are of Earth, but not of this time. We were genetically engineered, part-human and part-alien, and when the Eugenic Wars broke out, we didn't want to have any part in it and we fled. Your Starfleet Admiral happened to find my ship adrift in space, and when the ship's wards were breached I woke up - but I was weak from having been asleep for too long, and was overpowered."

"The Eugenic Wars? That was hundreds of years ago," Alec said, suddenly remembering their conversation in the pub.

"We have been sleeping for centuries, waiting for the sequencing of the matrix of the Genesis Device to be completed," Magnus explained.

It was a lot to process. Alec was still trying to wrap his head around it when Jace cut in, "That still doesn't justify you setting off a bomb in the middle of New York, killing a bunch of innocent people, then firing on a room full of unarmed Starfleet officers!"

"None of them were innocent," Magnus scoffed. "The building I bombed was a secret intelligence and research facility controlled by Valentine Morgenstern, and the Starfleet officers I killed were all part of Terra Prime." 

"All of them?" Alec asked challengingly, thinking of Hodge.  

"All of them," Magnus confirmed, meeting his gaze squarely.  

"How would you know?" Jace asked hotly.

"Because all of them stood around watching Valentine Morgenstern and his 'doctors' prod and poke at me to see what made me tick, what would make me bleed," Magnus said, voice shaking with barely-suppressed rage - the only time since his arrest that he'd showed any real emotion. 

"I'm sorry," Alec said quietly, thinking of all the scars on Magnus' body.

Magnus shook his head, and with some effort, seemed to come back to himself. "Your Admiral plans to murder every non-human or half-human who calls Earth home, to use the Genesis Device to wipe out all life on Earth while he and his faithful followers watch from the safety of the ship he forced me to help him build. So who's the monster now?"

"So you're saying you're the hero. A murderer serving a higher purpose," Jace said sarcastically.

"No, not a hero," Magnus said with a sardonic twist to his mouth. "I tried to smuggle my people to safety by concealing them in the weapons I designed, but when my plan was discovered I had no choice but to escape alone. When I sneaked back, all the torpedoes were gone. I thought Valentine Morgenstern had killed every single one of the people I hold most dear - or worse. No, my attack on Starfleet was purely vengeance."

"And how does Clarissa Morgenstern fit into all of this?" Alec asked.

"I was in the library and I heard him trying to speak to his crew. I was the one who helped him find them the first time, so he could hide them in the torpedoes," Clary said.

"Wait - what do you mean you heard him trying to speak to them? How could he talk to them if he didn't know where they were?" Jace asked.

Clary fidgeted. "I heard him inside my head."

"Huh?" Jace said.

Magnus closed his eyes, as if concentrating on something, and Jace jumped. "What the fuck?! Get out of my head! How did you do that?"

Magnus looked disappointed. "It seems that you are also susceptible." But Alec wasn't - whatever it was that Magnus could do, Alec was not one of the chosen few.

"Why should I trust that anything that you've said is true?" he asked Magnus.

"You shouldn't," Magnus replied easily, then made a strange gesture.

Then there was a flash of bright light and Alec must have blinked, and suddenly Magnus was standing right in front of him. He gasped in surprise when Magnus pushed him against the wall, his hand resting lightly at Alec's throat in a way that could turn deadly in a second.

"What the- step away from him!" Jace shouted, whipping out his phaser.

"I wouldn't do that. You might hurt your Captain instead," Magnus said, addressing Jace, but facing Alec with a half-smile that Alec couldn’t interpret. His body was pressed up against Alec in a way that reminded him far too much of a different time and a different place. Magnus leaned forward a little and for a moment Alec thought he was going to kiss him, but he seemed to think better of it and stepped back.

"You've gotten it wrong, First Officer Lightwood. The only reason that _you_ are still alive is because _I_ am allowing it," Magnus said pleasantly. "Now, if you don't mind, I would very much like to be reunited with my crew."

 

\--

 

Alec had been forced to call Izzy down from the medical bay into engineering, where the torpedoes were stored, on Magnus' insistence - or, more accurately, Izzy had cheerfully ignored Alec's veiled warnings, and breezed in with a charming smile for Magnus, too curious about their mysterious visitor to stay away. Despite himself, Alec couldn't hide his own curiosity as he watched Magnus open one of the torpedoes with nimble fingers. He placed a palm on what should have been the fuel compartment, and the shields around it slid out of sight to reveal some sort of transparent tube containing a sleeping man.

"Ragnor," Magnus said softly as he looked upon the pale face of the sleeping man, and Alec saw the tension go out of his shoulders. Magnus must have been so lonely, Alec couldn't help thinking. "He's my chief science officer."

"I've never seen technology like this. We haven't needed to freeze anyone since we developed warp capability," Izzy commented. "And your friend will be alright after he's been revived, even though he's been frozen for four hundred years?"

"The revival process will take at least half an hour. He will be very disoriented at first, and he will need to be given fluids, but slowly," Magnus replied as he tapped on a panel to start the revival process. "Thankfully, the alien race we owe part of our DNA to is quite resilient, but please be careful with him - with all of them. I should apologise in advance on his behalf though, Ragnor has never been a very good patient," Magnus said with a fond smile.

"Do you know what race was included in your makeup?" Izzy asked with interest.

"We are all a mix of this and that, but a large part of our DNA comes from a race known as the Q," Magnus said.

"Never heard of them," Alec admitted.

"You wouldn't have. According to the documents we found, they stick to their own part of the galaxy," Magnus said as he moved on to deactivate the next torpedo. "They have the ability to manipulate matter, energy, time, and space, and all of us inherited some of that ability."

"Is that how you escaped from the cell just now? And the jumpship?" Jace asked.

"We can teleport short distances, yes. From one side of cell to the other, and off the jumpship and onto the safety of ground. After that, I used a heavy-load transporter in an automated cargo station to get to an experimental transwarp device I had been working on to get myself out of Earth's orbit and onto Qo'noS, assuming that Morgenstern wasn't ready to risk war with the Klingons yet," Magnus admitted. "It should have burned out the device, but Valentine Morgenstern must have managed to divine the receiving point from the remnants of the machine."

The next person they uncovered was Magnus' second-in-command, a woman named Catarina. One by one, the torpedoes were opened and relieved of their precious cargo - men, women, children, the youngest of them a little girl who couldn't have been older than five. It made Alec sick to think that Valentine Morgenstern had essentially ordered the execution of all these people when he had demanded that Alec fire the torpedoes on Qo'noS. And for what crime? They hadn’t asked to be created, these human-alien hybrids that were forever doomed to be outcasts, mistrusted and feared for their differences. He was familiar with the historical records of the Eugenics Wars, and there were no Augments from that violent period of Earth’s history that matched the description of Magnus or his people. With their abilities, it would have been child’s play for them to wipe out their rivals, even the notorious tyrant Khan Noonien Singh - which led Alec to think that Magnus had been telling the truth about his people being peaceful and just wanting to be left alone.

Not all the torpedoes had been retrofitted with cryotubes, but Magnus picked out all the ones containing his crew with unerring accuracy. One of the torpedoes, however, contained neither the original fuel compartment nor a person. Instead, it held a glowing blue contraption, simmering with power - the Genesis Device.

"Best to leave it inside the torpedo case, I think," Alec suggested. "I assume that will make it easier to send the device to a suitable planet, when we find one."

Magnus looked at him in surprise. "Are you volunteering to help us find a suitable planet, Captain?"

"Yes - for the sake of your crew, who don't deserve to be hounded by those who want to exploit them for their powers," Alec replied. "And I will leave the information out of the captain's log, so that your people are left well alone."

"Mr By-the-Rules doctoring the captain's log and volunteering for an unsanctioned mission? Pigs are going to fly," Jace muttered.

"Thank you, Alexander," Magnus said quietly. He looked at Alec with regret in his eyes, and Alec dropped his gaze first. They would have to find a planet far away from Earth, preferably not within the same Quadrant of the galaxy, to minimise risk of discovery. Alec tried to tell himself that it was for the best.

Just then, Raphael spoke over the intercom. "Captain Lightwood, proximity alert - there's a ship at warp heading right for us."

"Klingons?" Jace asked.

"At warp?" Magnus said mockingly.

"It's the Admiral," Alec said with certainty, silently cursing himself for reporting Magnus' capture to Starfleet, when the Admiral definitely had the authority to intercept any incoming messages. "Jace, check with Maia to see how she's doing with that warp core. I'll stall for time."

"I'm coming with you," Clary immediately said. "The only thing that's going to stop him from destroying this ship is me."

Alec hesitated, then nodded, indicating that she should follow him to the bridge. 

"Shields at maximum, Mr Santiago, and we'll wait for them to make the first move."  



	5. Chapter 5

 

 

Alec got onto the bridge with Clary just in time to see a monstrous black ship drop out of warp and stop in front of the USS Archer, blocking the entire view forward. It bore a slight resemblance to a Federation starship in shape, but there was something menacing about the harsher lines of its reinforced hull. It was heavily armoured, with numerous blisters on its surface for weapons, and was at least four times bigger than the Archer, large enough to house an entire army. Alec had never seen a vessel like this in Starfleet’s arsenal - it wasn't a ship built for exploration, but for war.

"They are hailing us, Captain," Raphael reported. "Standard Starfleet intership communications frequency.”

"Contact Starfleet to report that we have been approached by an unmarked Federation vessel," Alec said.

"Can't do that, sir. With the warp core down, all auxiliary power has been diverted to the shields as you instructed," Raphael said.

It looked like they had no choice but to try to buy time until Maia had completed the delicate repairs on the core. "Alright, then. Accept their attempt at communication. Make sure it’s recorded and broadcast shipwide," Alec said grimly. The crew deserved to know firsthand the treachery of Valentine Morgenstern. 

The familiar face of the Admiral appeared on the forward screen. "Captain Lightwood," he greeted Alec cordially. 

"Admiral Morgenstern. That's some ship," Alec said. "What brings the head of Starfleet all the way out here?"

"I wasn't expecting to get word that you'd violated your orders to take the criminal out directly, and taken him into custody instead. What happened, son? What went wrong?" the Admiral asked, his condescending tone grating on Alec's last nerve.

"Our warp core malfunctioned unexpectedly, so we've had to improvise. We didn't even have enough power to fire those new torpedoes," Alec said innocently. Alec had expected the Admiral to maintain a poker face since he was much too experienced to show any tells, but to Alec's great unease, the Admiral seemed to relax.

"Is that so? How unfortunate. I hope you managed to secure your prisoner without too much trouble, then." 

"He didn't put up a fight," Alec said.

"So you spoke to him to get him to stand down? Did you find him to be a reasonable man?" Valentine Morgenstern asked.

"He did try to explain his reasons for doing what he did," Alec hedged.

Valentine Morgenstern shook his head regretfully. "I knew it was a bad idea to let you volunteer for this mission. You're too young and inexperienced, easily manipulated by his charm and lies. He's probably made me out to be the villain, cooked up some stories about my doubtless nefarious plans and painted himself as the victim forced into my servitude."

"That's interesting. During the meeting at Starfleet Command, you reported that he was a stranger with unknown motivations, but it sounds like you actually know him, Admiral," Alec said evenly.

The Admiral laughed. "You're too bright by half, I'll give you that. I know you are recording this conversation, Captain Lightwood. But what makes you think that you are going to get a chance to send that out? Your warp core is gone but your shields are up, so you have no power to spare for long distance communication. Even if you manage to get out of this alive, who do you think they will believe - the venerable Admiral, or the Captain of a ship full of half-human scum?" Valentine Morgenstern smiled nastily at Alec. "Did you know that your mother was once Ambassador to Vulcan?" 

Well, that certainly explained all the rumours. Alec saw red at what the Admiral was implying, but he took a deep breath and tried not to rise to the bait. "You might be the Admiral, but you're not going to be able to justify shooting down a Federation ship on a whim."

"Well, then. How about I tell you a story?" the Admiral said. "You and your crew went rogue and were found to be in league with a dangerous fugitive, harbouring him in enemy territory, leaving me no choice but to hunt you down and destroy you."

There were some panicked murmurs from the crew on the bridge, and Alec felt his heart sink. It was obvious that Valentine Morgenstern had never intended to spare the Archer. _Hurry up, Maia_.

"No, wait!" Clary cried. She stepped out so she was in clear view of the screen. "Father, stop, please!"

"Clarissa," Morgenstern looked angry, but not surprised. "I suspected that you'd managed to stow yourself on that ship."

"It's not just me," she said, terrified but still standing her ground. "I stole the Genesis Device as well." 

That certainly got the Admiral's attention. "You hid the Genesis Device inside one of the torpedoes, didn't you? You stupid girl!" the Admiral snarled. "I suspected that the creature had gotten his hooks into you, but I'd never imagined that you'd betray your own father like that."

"Captain, they're scanning our ship," Raphael murmured.

But the Archer's shields held, and the Admiral growled in frustration. "Enough of this nonsense, Lightwood. Give me my daughter and Genesis Device!"

"Why would I? Handing them over is as good as signing the death warrant for me and my crew," Alec pointed out.

Just then, the door to the bridge opened, and Magnus walked in with Jace.

"Admiral," Jace greeted their superior. "I'd say it's nice to see you, but I would be lying."

"Jace!" Alec hissed. "Now's not the time to antagonise-" then he startled when Magnus placed a hand on his arm and he suddenly heard Magnus' voice inside his head.

_Your sister and I figured out that physical touch could help those who are not susceptible to our speech of the mind hear us_ , Magnus explained. _Your engineer has completed the repairs, but the ship I built for Valentine Morgenstern is capable of Mark IV warp. She can out-run and out-gun your ship even at warp._

Out loud, Magnus told the Admiral, "The Genesis Device is useless to you without me activating it. I cannot hope to find justice at your hands, but I will surrender to you if you spare the crew of this ship. Your quarrel is with me, Valentine Morgenstern, not them."

Alec immediately understood why Clary had trusted Magnus over her own father. The connection with Magnus was a strange thing that went beyond speech - he could sense Magnus' intentions, how they didn't match the words he was saying to the Admiral because he knew that nothing would convince him to spare the crew of the Archer, and the intense loathing he had for the Admiral. It seemed that when Magnus and his people spoke through the mind, they were incapable of lying.

_The Mutara Nebula is at one-five-three-mark-four. If we go in there, the static discharge and gas will cloud our tactical display and disable the shields,_ Alec told Magnus. _We can't hide in there forever, but if Morgenstern is desperate enough to get his hands on the Genesis Device, he will have no choice but to follow. It would help to level the playing field._

"That is a surprisingly honourable offer from the likes of you - but I would be a fool to let you live, and even more so to let the crew of the Archer live," Valentine Morgenstern said. "Too many witnesses, too many potentially awkward questions... You only have two choices. Either you beam my daughter and the Genesis Device to me, and I make your deaths quick; or I target your life support systems located behind the aft nacelle. And after every single person aboard your ship suffocates, I will be free to retrieve the Genesis Device at my leisure." Morgenstern paused. "On second thought, keep the girl. I have no use for traitors."

Clary let out a shocked gasp, and Jace and Simon both made a noise of outrage.

Magnus moved a little closer to Simon and put a hand on his shoulder. Simon jumped a little, and looked around wildly at Alec; Alec gave him a slight nod, and Simon immediately started tapping on his console, locking in coordinates to their destination. 

"Lock phasers," the Admiral commanded his crew. "Last chance, Captain Lightwood - I am not a patient man."

"Mr Lewis, punch it!" Alec commanded.

The USS Archer fled, but within seconds Morgenstern's massive ship was hot on its heels. The Archer's proximity sensors screamed as the pursuing ship loomed behind them in the warp tunnel, but the nebula was only two minutes away... one minute...

They barreled into the vast cloud of glowing interstellar dust, static electricity crackling all around the starship like a lightning storm as it glided smoothly into the middle of it and swerved sharply upwards. Outside the nebula, the Admiral's ship came to a halt, hovering warily. 

"Captain, our shields have stopped functioning," Raphael noted.

"Shit! Lewis, what the hell were you thinking?" Jace exclaimed. "We have to get out here!"  

"No, I told him to bring us in here. It's part of the plan," Alec said.

"Sir, I must point out that even if entering the nebula disables their shields as well, our in-built weaponry are no match for theirs," Raphael said.

"Our in-built weaponry may be no match for theirs, but we do have 71 state-of-the-art photon torpedoes," Alec said. 

"But Maia said it might be dangerous to fire so many of them!" Jace protested.

"It's a risk we'll have to take," Alec said grimly.

"No, you don't have to risk the lives of your crew and mine," Magnus interrupted. "All you need is one torpedo, the one containing the Genesis Device."

"But you were going to use it to make a planet for your crew," Alec said.

"The location is not ideal," Magnus agreed. "But it's near enough to the Klingons that Federation ships are unlikely to venture here, and the Klingons are no match for us and will soon learn to leave us alone. The nebula will provide enough material to form the planet. I think it will do." 

"So you'll activate the device, we'll target it at his ship, and warp out of here," Alec said.

"No, with its fuel compartment removed, the torpedo is going to be moving far too slowly to be effective against Morgenstern. I can't risk Morgenstern realising what it is and warping out of the nebula before it detonates; I cannot allow him to live, with him knowing what he knows about my crew," Magnus said, his jaws set in determination. "He is a dangerous man with dangerous ideas, and it would benefit your people as well if he was dead." 

"Then what do you suggest?" Alec asked. 

"With their shields down, you'll be able to beam me onboard his ship with the device, will you not?"

Alec stared, horrified. "That’s a suicide mission!"

“Can’t you beam him there, then beam him back?” Clary asked timidly. 

“With all the static interference, it would be difficult enough to transport him on board the Admiral’s ship, much less accurately target and bring him back,” Raphael explained. 

"All my people will be fully awake soon, able to fend for themselves under Catarina's leadership, but if Morgenstern blows up this ship they will perish as well. I will do whatever I have to do to keep my people safe - and if my death will buy peace for my people, and continued peace for yours, then it will be well worth the price," Magnus said firmly. "I know you are not Vulcan, but have you not heard the Vulcan proverb? The needs of the many outweigh the needs of the few - or, in this case, the one."

Alec shook his head, speechless, but Raphael reminded them that time was running out when he reported, "Captain, they've entered the nebula. We might be able to evade them for a while, but it's only a matter of time before they find us."

"Alexander, this is the best chance we have of ending him, once and for all," Magnus said, then his voice softened. "And I will do it with or without your agreement - although of course I would much rather not have to do this alone." 

Alec swallowed hard, then tapped on his communicator. "Engineering, help me move the torpedo containing the Genesis Device to the transporter room. Dr Lightwood will point it out." He turned to Magnus. "I'll operate the transporter myself, and I'll get you where you need to go - I promise you that."

  

\--

  

They walked to the transporter room together, neither speaking a word. Alec had instructed Raphael to sneak up on the Admiral's ship from the bottom if he could, and keep a safe distance away - as long as it was within range for the transporter.

Engineering had already delivered the Genesis Device and between the two of them they managed to shift it onto the transporter.

"Captain, we are within range," Raphael reported over the ship's internal comms.

Alec fine-tuned the controls, brows furrowed in concentration. With tactical displays down, this was an operation he would trust no one with, and a burden on the conscience that he would not wish anyone else to bear. He'd been sent all the way out here by Admiral Morgenstern to execute Magnus, and after everything, that was exactly what he was going to end up doing after all. 

"It's ready," Alec finally said with a heavy heart. 

"You have three minutes before the Genesis Device detonates," Magnus told him, then seemed to read his mind even though they weren't in physical contact. "It's alright, Alexander. It was my choice, remember?"

"I know," Alec replied, unable to meet Magnus' eyes. 

Magnus stepped a little closer and touched Alec lightly on the arm. "I'm sorry I almost shot you at Starfleet Command." 

"I think you’ve evened that score a little when you saved us on Qo'noS," Alec pointed out, then added, "I'm sorry I crashed your jumpship."

Magnus smiled wryly. "You hardly need to apologise for fighting for your own survival. Not when I can't apologise for the decisions I have made to ensure the survival of my crew." He took a deep breath. "I hope you do not regret the night we spent together, even though my motivations for approaching you were far from pure. I want you to know that whatever we shared that night was as real for me as it was for you." 

Alec nodded jerkily, accepting the peace offering. 

"I don't expect you to forgive me," Magnus said. "I come from a time of war, while you have only known peace. We are from totally different worlds."

"Different centuries - although I suppose it comes down to the same thing," Alec agreed.

_For what it's worth, in another time and another place, I think we could have been something more, you and I_ , Magnus said softly into his mind, and kissed Alec. 

It was a gentle kiss, but the force of the emotions that came with it sent Alec reeling - all that regret, all that doubt, but also a bright spark of attraction; Magnus' admiration for Alec's intellect and sense of fairness, and the echo of that same kindred feeling Alec had almost thought he'd imagined. And Alec couldn't help feeding back into it, trying to let Magnus know that he felt the same. It was a kiss that laid bare all the possibilities between them, as well as all the impossibilities. 

Magnus stepped away reluctantly and got onto the transporter, then nodded at Alec. Alec forced himself to focus on the task at hand and pressed the activation button. The familiar set of lights began to swarm around Magnus and the torpedo, and he smiled at Alec before he disappeared.

Alec had barely had the time to process the confusing maelstrom of feelings plaguing him when a blast rocked the entire ship, sending Alec stumbling. He was struck by a new fear: had Magnus made it safely across with the Genesis Device?

"Alec, the Admiral's ship has found us!" Jace shouted over the comms.

"All decks prepare for imminent proximity detonation. Mr Santiago, damage report!" Alec barked into his communicator as he started running towards the bridge.

"We have a bulkhead breach, sir, but it's under control," Raphael replied.

Alec checked the time: two-and-a-half minutes to detonation. _Fuck._ "Mr Lewis, evasive manoeuvers, but stay within the nebula!"

The lights on the ship went out and the red emergency lights kicked in as all extra power on the USS Archer was diverted to shields; Alec blinked, trying to adjust to the low light washing everything with a nightmarish blood-red tint. All over the ship, the crew was scrambling to mitigate the damage that had been done to the ship, turning on airlock barriers to seal off areas that had been exposed to the deadly vacuum of space. Alec reached the bridge just as the next blast hit, throwing out the artificial gravity on the ship for a second and knocking everyone off their feet, but Alec managed to grab on and steady himself in the command chair. Magnus had trusted Alec with the lives of his crew, and the lives of Alec's own crew - his own family - were hanging in the balance. There was no damned way he was going to let them down. 

"Hull breach, starboard side," Raphael reported. 

_One-and-a-half minutes to detonation._  

"Mr Lewis, sharp left, then up, and get ready on my word," Alec said. 

_30 seconds._

"Hit it!" Alec shouted over the chaos in the room.

There was a sharp whine as the engines revved up, then the Archer shot out of the nebula like a bat out of hell.  

Behind them, the Admiral's ship seemed to be gearing up to give chase, when a burst of sudden light tore into the midsection of the ship as the Genesis Device finally detonated. Without the ship's shields holding the pieces in, debris from the ship flew in all directions from the explosion, then froze and started zooming back towards the point of the detonation as the light at the heart of the blast began to grow.

"Captain, I'm getting a reading I don't understand," Raphael said, the first time Alec had ever heard him sound uneasy. "The blast seems to be drawing us towards it, instead of pushing us away."

"Step on it - maximum warp, Mr Lewis," Alec said, gritting his teeth. 

They were slowing down even though they were in warp, and everybody on the ship could feel it. Alec was gripping the arm rests on the captain's chair so tightly that his knuckles were white. He could feel his entire ship shaking in the valiant effort to break free from the magnetic pull of the Genesis Device, but thankfully Alec had timed their escape just right. Like a cork pulling free from a bottleneck, the Archer zoomed forward with a sudden burst of speed when it finally got just out of reach from the effects of the explosion, and everyone heaved a sigh of relief. 

For Alec, with the relief of getting his crew and Magnus' crew to safety came a crushing ache in his chest. Magnus had successfully detonated the Device and saved them. That was it. He was... gone.  

"Hey, Lewis. I think we can slow down now," Jace said, and put a comforting hand on Alec's shoulder. "Right, Captain?" 

"Yeah," Alec agreed quietly, struggling to keep his expression neutral in front of his crew. 

The Archer came to a standstill a safe distance away, all the crew on the bridge leaving their stations to look at the forward view. The Genesis Device was drawing the entire nebula towards itself, a vivid whirlpool of blue and purple, alive and vibrant, in stark contrast with the emptiness of space all around them. Alec kept his eyes on the bright point of blue light at the heart of the explosion, and as he watched, the nebula swirled and coalesced into a sphere, spinning tighter and tighter until the light faded.

"Is it over?" Jace asked.

“Mr Lewis, bring us a little closer. Easy now,” Alec commanded.

As the Archer edged nearer cautiously, Alec saw that in place of the vast cloud that had been the Mutara Nebula, now there was a tiny blue planet that looked like a miniature version of Earth - the Genesis Planet.

"I think it's just begun," Alec replied.

 

 

 


	6. Epilogue

 

 

The medical bay was overflowing with patients who needed Izzy's attention - Magnus' crew, all 54 of them well on the way to recovery, and the members of Alec's crew who had been injured by the attack. Catarina, Magnus' second-in-command, turned out to be his chief medical officer as well, and as one of the first to be revived, she was soon up on her feet helping Izzy tend to the wounded.

Alec delivered the news of Magnus' death to her and Magnus' grumpy chief science officer personally, and both of them took the news with stoic resignation. But Catarina's 5-year-old daughter, who was taking a much longer time to recover because of her age, and who had clung to her mother for comfort the moment she'd been revived, suddenly mumbled with her face still buried in her mother's shirt, "Magnus isn't dead."

"He's gone, Madzie," she told her daughter gently.

"He isn't! I can still feel him," the little girl insisted. Catarina and Ragnor exchanged a look.

Alec looked to the both of them for answers, hardly daring to hope. 

"Some of our people are capable of psychometry - reading a person's or an object's history by touch," Catarina said hesitantly. "We have very little information on the Q, but by some records, it appears that they were almost omniscient."

"I suppose if anybody was going to have the bad manners to come back to life after breaking everybody's hearts by making some stupid noble sacrifice, it would be Magnus," Ragnor observed dryly.

"So you think he might have survived the detonation of the Genesis Device? That he's on the planet somewhere?" Alec asked. He wondered if that meant that Valentine Morgenstern and his crew had survived as well.

"Only one way to find out," Ragnor said.

 

\-- 

 

They took a Federation shuttle instead of the K'normian ship this time. The larger capacity allowed for a bigger landing crew - Alec, Jace, Catarina, a handful of Magnus' crew, and a troop of the Archer's security officers, in case of trouble.

"I am not sure what to expect," Catarina confessed. "The Device was meant to be fired at a planet rather than a nebula, although Magnus may have made some modifications after he was awakened."

"We have a replicator onboard that could provide your people with some necessities like food and clothing at least until you get your bearings, and we have a hydroponic greenhouse that could provide you with seedlings and saplings," Alec offered.

"That's very kind of you," Catarina said with a smile.

From the shuttle window, Alec saw stretches of deep blue oceans and towering mountains, and as they drew nearer to the surface of the planet, they found themselves crossing wide expanses of what looked like acres of tropical jungle, with fully grown trees and foliage, the thick vegetation making it impossible for them to land.

"I... I don't understand. This shouldn't be possible," Catarina said in astonishment.

"Either Magnus made some modifications to the original matrix, or..." Alec paused, thinking. "Magnus mentioned that Valentine Morgenstern intended to wipe out all life on Earth while his followers stayed on his ship. Perhaps his ship contained functions to provide for a large population for a sustained amount of time - larger scale hydroponics, bio-matter resequencers, emergency provisions. And all these contributed to the formation of the planet as it is."

The shuttle's sensors did however detect a single life sign belonging to a living organism more complex than vegetation. With some effort, they finally found a small clearing big enough for them to land on the bank of a river. Picking their way through the abundant undergrowth and hacking through low-hanging vines, they followed the signal to a rocky, mountainous area riddled with caves, then deeper into the bowels of the planet.

Unlike caves on Qo'noS, these caves were cavernous halls of damp limestone; a stream ran through all of it, the water alternating from knee-deep dark water to a slimy trickle. Alec's torch flashed across the ceiling, and he frowned at the rows of stalactites dripping down like many needle-like teeth - those structures looked like they should have taken decades, if not centuries to form. The cave began to slope uphill, the floor getting drier, then completely dry; until they saw a blue light in the distant darkness reminiscent of the glow from the Genesis Device. 

It was a glowing blue crystal, propped up by gigantic stalagmites like a jewel set in the ground. The material was translucent, like smoky quartz, and right in the middle of it was a vaguely humanoid shape, curled up in a foetal position. 

"Holy fuck," Jace mumbled. "How do we get him out of there?" 

For a long time, nobody had any reply. None of them had pickaxes or drills to get through the material, and Alec dreaded the thought of breaking through the crystal to find that all they had on their hands was a corpse - a dread that he knew was also on the minds of Magnus' crew. Except that their sensors showed that whatever was inside there was very much alive.

Catarina placed her palm tentatively on the crystal; there was a pulse that went through the whole material, and inside the figure stirred.

"Memories," she gasped in surprise. "I think we need to wake him with our memories of him."

One by one, Magnus' crew stepped up to surround the odd crystal and began to send pulse after pulse of memories into it. Happy memories? Sad memories? Memories of love, laughter, and better times? Alec held his breath, hoping against hope as each pulse drew a stronger reaction from the figure inside the crystal.

Jace nudged Alec. "Maybe you ought to join in."

"Me?" Alec baulked and shook his head.

"You're the only one with proper memories of him from after Morgenstern woke him up," Jace pointed out.

"I think most of those memories might be ones he'd rather forget," Alec said quietly.

The crystal began to crack, fissures spreading through the material. When the first crack finally reached the figure inside, it shuddered; then the entire crystal shattered suddenly. Alec darted forward instinctively, but it was Magnus' crew who caught him.

Magnus opened his eyes, blinking in the dim light as he looked at the faces around him. "Catarina? Elias? Where am I?"

Alec shifted his weight, and the movement caught Magnus' eye. He looked at Alec for what felt like a long time, cat eyes blinking in the semi-darkness, then winced in pain and grabbed his head.

"I... who are you?" Magnus asked.

 

\-- 

 

"My sister is not familiar with your physiology. In your professional opinion, will he ever regain his memories?" Alec asked Catarina.

"I do not know. I assume his Q DNA had something to do with him surviving being torn apart on a subatomic level, but how much of him is as he once was? This is uncharted territory even for us," Catarina admitted. "He seems to be able to recognise some of us, mainly those who were close to him, and has some memories of the time before we left Earth. But even then those memories are hazy at best. And I'm not just saying this because I am trying to spare him from the punishment your Federation probably thinks he deserves for killing all those people."

"No, I wasn't trying to imply that," Alec said quickly.

Catarina smiled at Alec kindly. "It's alright, Captain Lightwood. Contrary to what you may think, we are not savages. We, too, have our own laws, social structures and ethical conundrums that Ragnor, Magnus, and I discussed late into the night..." She sighed. "Magnus was - _is_ \- an incredibly generous soul. But when the wars broke out, he did what he thought he had to do, what he thought was best for us, at the cost of his own heart. I wish you'd had the chance to know him properly."

"I wish I had, too," Alec said.

"I understand that you are returning to Earth immediately," she said.

Alec nodded. "Your crew is settled in. The longer we linger, the higher the chances that Starfleet will send out reinforcements to find out what happened between us and the Admiral."

They were in one of the Starfleet-issue modular shelters from the USS Archer that Alec had managed to spare from the stores while Magnus' crew constructed their own buildings, now designated as a temporary office. Alec had also given them the seedlings and provisions as promised, and the K'normian trade craft - he'd done all he could for them without raising suspicion.

"You're leaving without saying goodbye to Magnus?" Catarina asked him, and Alec nodded.

"I think it would be for the best."

Catarina insisted on seeing him out to the shuttle, but when they opened the door, they found Magnus standing outside waiting for them. Catarina smiled and made herself scarce, leaving Alec standing there staring at Magnus in silence.

"Were you just going to go?" Magnus asked.

"I... yeah."

"I get the feeling, from the way everybody has been reacting, that I'm supposed to know you," Magnus said. "Your blond crew mate keeps glaring at me like I've done something terrible."

"That's just his face," Alec muttered, and Magnus laughed brightly, a wholly foreign sound. Alec cleared his throat. "Did you need me for something?"

Magnus shrugged. "I wanted to see you again."

"Why?"

"Does one need a reason to appreciate beauty?" Magnus asked with a mischievous grin.

"I'm sorry. I have to go," Alec said, and quickly started to walk away from this Magnus who couldn't remember him but was still trying to flirt with him, the pain of being near him too much for Alec to handle right now.

"Alexander?"

Alec froze. He turned around to find Magnus frowning at him and rubbing his temple absently.

"That's your name, isn't it?"

Alec took a deep breath, then let it out again. "It's Captain Lightwood," he said, then turned away and kept on walking.

 

\--

 

Once the Archer was properly Earthbound, Alec made his way to his private quarters, desperately in need of some time away from everyone, and was only mildly surprised to find his sister waiting for him. Izzy always knew.

"Izzy? If it's not urgent, could you-"

"I need to talk to you," she insisted.

Alec let her in reluctantly. "What's wrong?" he asked her.

"What's wrong? Oh, Alec," she sighed. "Well, Starfleet Medical Code states that the treatment of a patient is to be determined at the discretion of his attending physician, which is me. And you need to talk to someone before you explode."

"I'm fine, Iz."

"You're really not. Who do you think you’re fooling?"

Alec shook his head, but Izzy just stood there patiently. "Izzy, did I make the right decision not to take Magnus into custody?" Alec finally asked.

"Talk it through with me," Izzy suggested. "What were the logical reasons for letting Magnus go?"

"He doesn't remember anything from after he woke up from the cryotube. How can I make a man stand trial for crimes he doesn't remember committing?" Alec asked in frustration. "He can't give any testimony that makes sense, and all I know are bits and pieces of the whole story. The only other person who knew what was going on was Admiral Morgenstern, and he's dead. It would be a farce of a trial, a waste of everybody's time."

"And what about the other reasons?" Izzy prodded gently. "The ones that have nothing to do with logic?"

Alec hesitated. "He has a chance at a new life. A life of peace. I can't... I can't take that away. It feels like the wrong thing to do."

"Alec, we're only human. Sometimes a feeling is all we have to go on," Izzy told him, and gave him a hug. "And you know what? I have a feeling too - I think we haven't seen the last of Genesis Planet."

 

\--

 

  
_Captain's log, Stardate 2259.59_

_Starship Archer returning to Earth following an altercation with Admiral Morgenstern, and the discovery of a treacherous plot against the Federation. We managed to emerge victorious, but our incursion on Qo'noS will not have gone unnoticed by the Klingons, and I fear that this is just the beginning of some bigger trouble in the not too distant future._

_Our original mission, to arrest the man who attacked Starfleet Command, was a failure as well - he is dead, although not by our hands. He gave his life so the rest of us could live. He said he wasn't a hero, but he was a man caught out of his own time, and he did the best he could, and I suppose in the end that's the most we can ask of anybody. Some will disagree. But I can only say this: of all the souls I have known, his burned the brightest - at least for me._

_Alec Lightwood out._

**Notes for the Chapter:**

> Please hold. Plotting of sequel in progress...
> 
> (I'm not that evil to end this story like this, c'mon.)
> 
> In the meantime, do check out the other fics from the [Shadowhunters Hiatus Big Bang](https://shhiatusbang.tumblr.com). They'll be posted gradually over the week! :)

**Works inspired by this one:**

  * [Of All The Souls I Have Known](https://archiveofourown.org/works/15650931) by [Catastrokey (orphan_account)](https://archiveofourown.org/users/orphan_account/pseuds/Catastrokey)




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